Different index than annotated genome scRNA-seq/troubleshooting : bioinformatics

Hi All, When pre-processing scRNA-seq data I have accidentally used different indexes (Hg19) for alignment in comparison to the gene annotation file I used for count quantification (GRCh38).

I am using publically available data and my workflow seems to have achieved the same/better levels of alignment (~70%) than the original study, however I am detecting far fewer (average 2500 Vs average 3500) non-0 expressed genes per cell. Could this mistake be a reason for less genes being detected? If not, what other troubleshooting steps can I take to figure out why I am detecting less genes. For reference I am using Galaxy until I can get access to University servers.

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